Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate WP_012475425.1 CPHAMN1_RS10190 type 1 glutamine amidotransferase
Query= SwissProt::P00901 (198 letters) >NCBI__GCF_000020545.1:WP_012475425.1 Length = 187 Score = 234 bits (596), Expect = 9e-67 Identities = 110/190 (57%), Positives = 148/190 (77%), Gaps = 5/190 (2%) Query: 2 LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61 ++++IDNYDSFTYN+VQY+GELGA+V V RNDE+T+A + PE+IV+SPGP TP AG Sbjct: 1 MVLVIDNYDSFTYNLVQYMGELGADVDVARNDEVTVADVLDRKPEKIVISPGPGTPENAG 60 Query: 62 VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121 +S++ I G++P+LGVCLGHQ+IG+A GG VVRAR +MHGKTS ++H + G+F G++N Sbjct: 61 ISVQLIRSVEGRIPLLGVCLGHQAIGEALGGKVVRARDIMHGKTSLIYHDNQGIFAGIDN 120 Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181 P TRYHSL+V+RETLP+ L V AWT ED IMG+ ++LN+ GVQFHPESI+T Sbjct: 121 PFIATRYHSLIVERETLPEELTVRAWT--EDRI---IMGMDCRSLNLYGVQFHPESIMTR 175 Query: 182 QGHELFANFL 191 +G ++ NFL Sbjct: 176 EGKQIIRNFL 185 Lambda K H 0.320 0.138 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 166 Number of extensions: 4 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 198 Length of database: 187 Length adjustment: 20 Effective length of query: 178 Effective length of database: 167 Effective search space: 29726 Effective search space used: 29726 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 44 (21.6 bits)
Align candidate WP_012475425.1 CPHAMN1_RS10190 (type 1 glutamine amidotransferase)
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00566.hmm # target sequence database: /tmp/gapView.1313.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00566 [M=192] Accession: TIGR00566 Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-79 249.7 0.0 1.1e-78 249.5 0.0 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012475425.1 CPHAMN1_RS10190 type 1 glutamine Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012475425.1 CPHAMN1_RS10190 type 1 glutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.5 0.0 1.1e-78 1.1e-78 1 191 [. 1 186 [. 1 187 [] 0.99 Alignments for each domain: == domain 1 score: 249.5 bits; conditional E-value: 1.1e-78 TIGR00566 1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaisslelie 69 mvl+idnydsftynlvq++ elga+v v rnd++t++++ + +p++ ivisPGP+tP++a+is ++li+ lcl|NCBI__GCF_000020545.1:WP_012475425.1 1 MVLVIDNYDSFTYNLVQYMGELGADVDVARNDEVTVADVLDRKPEK-IVISPGPGTPENAGIS-VQLIR 67 79********************************************.****************.***** PP TIGR00566 70 hlaGklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvvea 138 + G++P+lGvClGhqa++ a G++vvra+ ++hGk+s i h+++++fag+ nP + atryhsl+ve lcl|NCBI__GCF_000020545.1:WP_012475425.1 68 SVEGRIPLLGVCLGHQAIGEALGGKVVRARDIMHGKTSLIYHDNQGIFAGIDNP--FIATRYHSLIVER 134 ******************************************************..************* PP TIGR00566 139 etldtllevtaleeeeieimairhrdlpleGvqfhPesilselGkellanflk 191 etl++ l+v a++e + im++ r l+l GvqfhPesi++ +Gk++++nfl+ lcl|NCBI__GCF_000020545.1:WP_012475425.1 135 ETLPEELTVRAWTEDR-IIMGMDCRSLNLYGVQFHPESIMTREGKQIIRNFLD 186 *************999.9*********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (192 nodes) Target sequences: 1 (187 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.98 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory